Project Summary Different human mutations in the photoreceptor-specific gene Crx are linked with multiple retinopathies that vary in their severity and age of onset. How different mutations in this single gene lead to different pathologies is not well understood. Because CRX is a transcription factor, these disease mutations must act by altering the ability of CRX to regulate gene expression. Our goal is to understand how different classes of CRX mutations modify its regulatory function. To achieve this, we will apply a recently developed massively parallel reporter gene technology to systematically and comprehensively measure CRX regulatory function in live retina from multiple mouse knock-in models that carry human CRX disease mutations. We will use the data to train and test a mechanistic, quantitative model that describes how CRX mutations alter protein-DNA and protein-protein interactions to modify gene regulation. In a complementary approach, we will use the knock-in mouse models to determine the effects of CRX disease mutations on its in vivo genome-wide binding, and on the binding of the cooperatively interacting transcription factors OTX2, NRL, and NR2E3. Using these two approaches, we aim to understand how different classes of CRX disease mutations modify gene regulation in photoreceptors, and discover new mechanisms of disease pathogenesis. Our results will provide a strong basis for classifying new CRX mutations, and for designing targeted therapies to treat different genetic forms of retinopathy.